Not really. तुमको क्या चाहिए (can also be written तुम्हें क्या चाहिए) may be directed towards a person of either gender. It could mean 'What do you want' but the meaning is closer to 'What do you need?'. Basically, it conveys a stronger sentiment.

As you say, तुम क्या चाहती हो? is directed towards a female person due to the feminine form of the verb. The masculine form would be 'तुम क्या चाहते हो?'. Both of these mean 'What do you want?'.